Part I: In Situ Detection of RNA Molecules Using FISH Techniques
1. Tagging and Application of RNA Probes for Sequence-Specific Visualization of RNAs by Fluorescent In Situ Hybridization
Thomas Dresselhaus and Andrea Bleckmann
2. Quantitative Fluorescence In Situ Hybridization Detection of Plant mRNAs with Single-Molecule Resolution
Kun Huang, Mona Batish, Chong Teng, Alex Harkess, Blake C. Meyers, and Jeffrey L. Caplan
3. Visualization of Endoplasmic Reticulum-Associated mRNA in Mammalian Cells
Jingze J. Wu and Alexander F. Palazzo
4. Simultaneous Detection of mRNA and Protein in S. cerevisiae by Single Molecule FISH and Immunofluorescence
Evelina Tutucci and Robert H. Singer
Part II: In Vivo Imaging of RNA Transport and Localization
5. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More
Michael Ryckelynck
6. Visualization of Transiently Expressed mRNA in Plants Using MS2
Eduardo Jos Pe a and Manfred Heinlein
7. New Generations of MS2 Variants and MCP Fusions to Detect Single mRNAs in Living Eukaryotic Cells
Xavier Pichon, Marie-C cile Robert, Edouard Bertrand, Robert H. Singer, and Evelina Tutucci
8. In Vivo Imaging of Mobile mRNAs in Plants Using MS2
Kai-Ren Luo, Nien-Chen Huang, and Tien-Shin Yu
9. RNA Imaging with RNase-Inactivated Csy4 in Plants and Filamentous Fungi
David Burnett, Alexander Lichius, and Jens Tilsner
Part III: Imaging and Analysis of RNA Uptake and Transport between Cells
10. Utilizing Potato Virus X to Monitor RNA Movement
Zhiming Yu, Sung Ki Cho, Pengcheng Zhang, Yiguo Hong, and David J. Hannapel
11. A Protocol for Non-Biased Identification of RNAs Transferred between Heterologous Mammalian Cell Types Using RNA Tagging, Cell Sorting, and Sequencing
Sandipan Dasgupta and Jeffrey E. Gerst
12. Synthesizing Fluorescently Labeled dsRNAs and sRNAs to Visualize Fungal RNA Uptake
Rachael Hamby, Ming Wang, Lulu Qiao, and Hailing Jin
13. Labeling of dsRNA for Fungal Uptake Detection Analysis
Matteo Galli, Jafargholi Imani, and Karl-Heinz Kogel
Part IV: Identification and Analysis of RNA-Binding Proteins
14. Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs)
Mengge Shan and Brian D. Gregory
15. Plant Individual Nucleotide Resolution Crosslinking and Immunoprecipitation to Characterize RNA-Protein Complexes